Parameters Input values
Folder name : Example data
Sequence name : CDH1
Reference genome : BSgenome.Hsapiens.UCSC.hg19
Type of experiment : Direct-BSP
Group order : Low methylated DNA, High methylated DNA
Date of analysis : 2023-06-09 17:25

Files content

Data files content

Parameters Data files content
Sequence name : CDH1
Collections :
Groups : Low methylated DNA, High methylated DNA
Replicates : 1, 2, 3

Data files paths

File paths used for the analysis

D:/Documents/These/ABSP/results/Example data/CDH1/individual_results_direct/data/CDH1_High methylated DNA_1_methdata.csv
D:/Documents/These/ABSP/results/Example data/CDH1/individual_results_direct/data/CDH1_High methylated DNA_2_methdata.csv
D:/Documents/These/ABSP/results/Example data/CDH1/individual_results_direct/data/CDH1_High methylated DNA_3_methdata.csv
D:/Documents/These/ABSP/results/Example data/CDH1/individual_results_direct/data/CDH1_Low methylated DNA_1_methdata.csv
D:/Documents/These/ABSP/results/Example data/CDH1/individual_results_direct/data/CDH1_Low methylated DNA_2_methdata.csv
D:/Documents/These/ABSP/results/Example data/CDH1/individual_results_direct/data/CDH1_Low methylated DNA_3_methdata.csv

Methylation data

Methylation data of replicates

chr16:68771035-68771036 chr16:68771037-68771038 chr16:68771045-68771046 chr16:68771051-68771052 chr16:68771059-68771060 chr16:68771064-68771065 chr16:68771073-68771074 chr16:68771090-68771091 chr16:68771092-68771093 chr16:68771112-68771113 chr16:68771138-68771139 chr16:68771143-68771144 chr16:68771150-68771151 chr16:68771159-68771160 chr16:68771182-68771183 chr16:68771200-68771201 chr16:68771203-68771204 Mean SD
Low methylated DNA 1 0.00 0.00 0 0.00 0.000 6.00 0.00 0.00 0 0.00 0 1.69 1.98 NA NA NA NA 0.74 1.72
Low methylated DNA 2 13.16 1.33 0 1.40 0.000 3.40 0.00 0.00 0 0.00 0 23.22 NA NA NA NA NA 3.54 7.24
Low methylated DNA 3 0.00 0.00 0 0.00 0.000 0.00 0.00 0.00 0 0.00 0 0.00 NA NA NA NA NA 0.00 0.00
High methylated DNA 1 81.43 100.00 100 83.35 100.000 95.72 77.22 97.52 100 99.63 100 100.00 100.00 NA NA NA NA 94.99 8.36
High methylated DNA 2 83.50 100.00 100 84.08 100.000 95.84 77.83 98.55 100 99.73 100 100.00 100.00 NA NA NA NA 95.35 7.93
High methylated DNA 3 96.39 100.00 100 76.89 91.865 98.21 74.25 99.56 100 99.90 100 100.00 100.00 99.62 100 100 100 96.28 8.08

Methylation data of groups

chr16:68771035-68771036 chr16:68771037-68771038 chr16:68771045-68771046 chr16:68771051-68771052 chr16:68771059-68771060 chr16:68771064-68771065 chr16:68771073-68771074 chr16:68771090-68771091 chr16:68771092-68771093 chr16:68771112-68771113 chr16:68771138-68771139 chr16:68771143-68771144 chr16:68771150-68771151 chr16:68771159-68771160 chr16:68771182-68771183 chr16:68771200-68771201 chr16:68771203-68771204 Mean SD
Low methylated DNA 4.39 0.44 0 0.47 0.00 3.13 0.00 0.00 0 0.00 0 8.3 1.98 NaN NaN NaN NaN 1.44 2.51
High methylated DNA 87.11 100.00 100 81.44 97.29 96.59 76.43 98.54 100 99.75 100 100.0 100.00 99.62 100 100 100 96.28 7.30

Plots of replicates

Lollipop plots

Sample order : as-is

Type : proportional

Type : condensed

Genomic plots

Sample order : as-is

Plots of groups

Lollipop plots

Sample order : as-is

Type : proportional

Type : condensed

Genomic plots

Sample order : as-is

Statistics

Descriptive statistics of groups

Methylation means of all CpG positions

Collection Group N Methylation mean SD SEM Confidence interval of 95% (±)
Low methylated DNA 3 1.43 1.87 1.08 4.64
High methylated DNA 3 95.54 0.67 0.38 1.65

Methylation by CpG positions

CpG number CpG coordinate Collection Group N Methylation mean SD SEM Confidence interval of 95% (±)
1 chr16:68771035-68771036 Low methylated DNA 3 4.39 7.60 4.39 18.87
1 chr16:68771035-68771036 High methylated DNA 3 87.11 8.11 4.68 20.14
2 chr16:68771037-68771038 Low methylated DNA 3 0.44 0.77 0.44 1.91
2 chr16:68771037-68771038 High methylated DNA 3 100.00 0.00 0.00 0.00
3 chr16:68771045-68771046 Low methylated DNA 3 0.00 0.00 0.00 0.00
3 chr16:68771045-68771046 High methylated DNA 3 100.00 0.00 0.00 0.00
4 chr16:68771051-68771052 Low methylated DNA 3 0.47 0.81 0.47 2.01
4 chr16:68771051-68771052 High methylated DNA 3 81.44 3.96 2.28 9.83
5 chr16:68771059-68771060 Low methylated DNA 3 0.00 0.00 0.00 0.00
5 chr16:68771059-68771060 High methylated DNA 3 97.29 4.70 2.71 11.67
6 chr16:68771064-68771065 Low methylated DNA 3 3.13 3.01 1.74 7.47
6 chr16:68771064-68771065 High methylated DNA 3 96.59 1.40 0.81 3.49
7 chr16:68771073-68771074 Low methylated DNA 3 0.00 0.00 0.00 0.00
7 chr16:68771073-68771074 High methylated DNA 3 76.43 1.92 1.11 4.76
8 chr16:68771090-68771091 Low methylated DNA 3 0.00 0.00 0.00 0.00
8 chr16:68771090-68771091 High methylated DNA 3 98.54 1.02 0.59 2.53
9 chr16:68771092-68771093 Low methylated DNA 3 0.00 0.00 0.00 0.00
9 chr16:68771092-68771093 High methylated DNA 3 100.00 0.00 0.00 0.00
10 chr16:68771112-68771113 Low methylated DNA 3 0.00 0.00 0.00 0.00
10 chr16:68771112-68771113 High methylated DNA 3 99.75 0.14 0.08 0.34
11 chr16:68771138-68771139 Low methylated DNA 3 0.00 0.00 0.00 0.00
11 chr16:68771138-68771139 High methylated DNA 3 100.00 0.00 0.00 0.00
12 chr16:68771143-68771144 Low methylated DNA 3 8.30 12.95 7.47 32.16
12 chr16:68771143-68771144 High methylated DNA 3 100.00 0.00 0.00 0.00
13 chr16:68771150-68771151 Low methylated DNA 1 1.98 NA NA NaN
13 chr16:68771150-68771151 High methylated DNA 3 100.00 0.00 0.00 0.00
14 chr16:68771159-68771160 Low methylated DNA 0 NaN NA NA NaN
14 chr16:68771159-68771160 High methylated DNA 1 99.62 NA NA NaN
15 chr16:68771182-68771183 Low methylated DNA 0 NaN NA NA NaN
15 chr16:68771182-68771183 High methylated DNA 1 100.00 NA NA NaN
16 chr16:68771200-68771201 Low methylated DNA 0 NaN NA NA NaN
16 chr16:68771200-68771201 High methylated DNA 1 100.00 NA NA NaN
17 chr16:68771203-68771204 Low methylated DNA 0 NaN NA NA NaN
17 chr16:68771203-68771204 High methylated DNA 1 100.00 NA NA NaN

Student’s T test

For means of CpG positions

Student’s T test (two-samples, unpaired).

Collection Compared group 1 Compared group 2 N group 1 N group 2 p-value p-value significance level
Low methylated DNA High methylated DNA 3 3 2.34e-05 ****

For each CpG position

ERROR: ℹ In argument: data = map(.data$data, .f, ...). Caused by error in map(): ℹ In index: 1. Caused by error in t.test.default(): ! les données sont pratiquement constantes ERROR: ℹ In argument: data = map(.data$data, .f, ...). Caused by error in map(): ℹ In index: 1. Caused by error in t.test.default(): ! les données sont pratiquement constantes ERROR: ℹ In argument: data = map(.data$data, .f, ...). Caused by error in map(): ℹ In index: 1. Caused by error in t.test.default(): ! les données sont pratiquement constantes ERROR: ℹ In argument: data = map(.data$data, .f, ...). Caused by error in map(): ℹ In index: 1. Caused by error in t.test.default(): ! nombre d’observations ‘x’ insuffisant ERROR: ℹ In argument: data = map(.data$data, .f, ...). Caused by error in map(): ℹ In index: 1. Caused by error in t.test.default(): ! nombre d’observations ‘x’ insuffisant ERROR: ℹ In argument: data = map(.data$data, .f, ...). Caused by error in map(): ℹ In index: 1. Caused by error in t.test.default(): ! nombre d’observations ‘x’ insuffisant ERROR: ℹ In argument: data = map(.data$data, .f, ...). Caused by error in map(): ℹ In index: 1. Caused by error in t.test.default(): ! nombre d’observations ‘x’ insuffisant ERROR: ℹ In argument: data = map(.data$data, .f, ...). Caused by error in map(): ℹ In index: 1. Caused by error in t.test.default(): ! nombre d’observations ‘x’ insuffisant

Warning: CpG sites 3, 9, 11, 13, 14, 15, 16, 17 are removed as T test can not be performed due to N<3 for at least one group or essentially constant data between two groups.

Student’s T test (two-samples, unpaired).

CpG number CpG coordinate Collection Compared group 1 Compared group 2 N group 1 N group 2 p-value p-value significance level
1 chr16:68771035-68771036 Low methylated DNA High methylated DNA 3 3 2.14e-04 ***
2 chr16:68771037-68771038 Low methylated DNA High methylated DNA 3 3 1.98e-05 ****
4 chr16:68771051-68771052 Low methylated DNA High methylated DNA 3 3 5.14e-04 ***
5 chr16:68771059-68771060 Low methylated DNA High methylated DNA 3 3 7.76e-04 ***
6 chr16:68771064-68771065 Low methylated DNA High methylated DNA 3 3 3.15e-05 ****
7 chr16:68771073-68771074 Low methylated DNA High methylated DNA 3 3 2.09e-04 ***
8 chr16:68771090-68771091 Low methylated DNA High methylated DNA 3 3 3.57e-05 ****
10 chr16:68771112-68771113 Low methylated DNA High methylated DNA 3 3 6.24e-07 ****
12 chr16:68771143-68771144 Low methylated DNA High methylated DNA 3 3 6.58e-03 **

Boxplots

For means of CpG positions

Boxplots represent methylation median and quartiles of each group with errors bars. Methylation mean are represented as diamond shapes.

The p-values and p-value significance levels are determined by Student's T tests (two-samples, unpaired).

p-values significance levels

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p-values

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without p-values

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For each CpG position

Boxplots represent methylation median and quartiles of each group with errors bars. Methylation mean are represented as diamond shapes.

The p-values and p-value significance levels are determined by Student's T tests (two-samples, unpaired).

p-values significance levels

Open boxplot image in a new tab.

p-values

Open boxplot image in a new tab.

without p-values

Open boxplot image in a new tab.

Methylation profile plots

Each points represent the methylation mean of clones or replicates for a given CpG site.
The p-values and p-value significance levels are determined by Kruskal-Wallis tests.

Type : proportional

p-values significance levels

p-values

without p-values

Type : condensed

p-values significance levels

p-values

without p-values

Output data

Directories